Cell Ranger

Overview

Cell Ranger is the official analysis pipeline from 10x Genomics for processing Chromium single-cell gene expression data. It performs FASTQ generation, read alignment to a reference transcriptome, barcode and UMI counting, and cell-by-gene matrix construction. Cell Ranger also runs secondary analyses including dimensionality reduction, clustering, and differential expression, providing web-viewable summary reports for rapid quality assessment.

Installation

Download the latest release from the 10x Genomics support site. After extracting the archive, add the cellranger binary to your PATH:

tar -xzf cellranger-8.0.1.tar.gz
export PATH=$PWD/cellranger-8.0.1:$PATH

Cell Ranger is not available through Bioconda. A 10x-compatible reference package is also required (e.g., refdata-gex-GRCh38-2024-A).

Basic Usage

Run the count pipeline to align reads and generate the filtered feature-barcode matrix for a single sample.

cellranger count --id=sample1 \
  --transcriptome=/ref/refdata-gex-GRCh38-2024-A \
  --fastqs=/data/sample1/ \
  --sample=sample1 \
  --localcores=16 --localmem=64

Cell Ranger auto-detects chemistry by default. If multiple FASTQ directories exist for the same sample, provide them as a comma-separated list to --fastqs.

Key Parameters

Flag / option	Description
`--id`	A unique run ID; Cell Ranger creates an output directory with this name.
`--transcriptome`	Path to the Cell Ranger-compatible reference transcriptome directory.
`--fastqs`	Path to the directory containing FASTQ files (or a comma-separated list of directories).
`--sample`	Sample name prefix as it appears in the FASTQ file names.
`--localcores`	Maximum number of CPU cores to use (default: all available).
`--localmem`	Maximum memory in GB to use (default: 90% of system memory).
`--expect-cells`	Expected number of recovered cells (default: 3000). Cell Ranger uses this as a hint for cell calling.
`--chemistry`	Assay chemistry (e.g., `SC3Pv3`). Usually auto-detected.
`--include-introns`	Count reads mapping to introns (enabled by default since Cell Ranger 7.0 for single-nuclei data).

Expected Output

Cell Ranger creates a directory named after the --id value. Key outputs include:

outs/filtered_feature_bc_matrix/ – the filtered cell-by-gene count matrix in Market Exchange format (MEX), containing barcodes that Cell Ranger identified as valid cells.
outs/raw_feature_bc_matrix/ – the unfiltered count matrix for all detected barcodes.
outs/possorted_genome_bam.bam – coordinate-sorted BAM file with cell-barcode and UMI tags.
outs/web_summary.html – interactive HTML report with sequencing quality, mapping statistics, and preliminary clustering results.
outs/metrics_summary.csv – tab-delimited summary of key metrics (estimated cells, reads per cell, median genes per cell, etc.).